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Genome-wide view and characterization of natural antisense transcripts in Cannabis Sativa L

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Abstract

Natural Antisense Transcripts (NATs) are a kind of complex regulatory RNAs that play crucial roles in gene expression and regulation. However, the NATs in Cannabis Sativa L., a widely economic and medicinal plant rich in cannabinoids remain unknown. In this study, we comprehensively predicted C. sativa NATs genome-wide using strand-specific RNA sequencing (ssRNA-Seq) data, and validated the expression profiles by strand-specific quantitative reverse transcription PCR (ssRT-qPCR). Consequently, a total of 307 NATs were predicted in C. sativa, including 104 cis- and 203 trans- NATs. Functional enrichment analysis demonstrated the potential involvement of the C. sativa NATs in DNA polymerase activity, RNA-DNA hybrid ribonuclease activity, and nucleic acid binding. Finally, 18 cis- and 376 trans- NAT-ST pairs were predicted to produce 621 cis- and 5,679 trans- small interfering RNA (nat-siRNAs), respectively. These nat-siRNAs were potentially involved in the biosynthesis of cannabinoids and cellulose. All these results will shed light on the regulation of NATs and nat-siRNAs in C. sativa.

Key message

In C. sativa, NATs potentially participated in genetic information processes, growth and development, stress resistance, and the biosynthesis of compounds. Nat-siRNAs were potentially involved in the biosynthesis of CBDs and cellulose.

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Data availability

The RNA-Seq raw data of leaves, roots, and stems have been deposited into the SRA database with the accession numbers SRR17817906, SRR17817907, and SRR17817908, respectively.

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Funding

This work was supported by the Chinese Academy of Medical Sciences Innovation Funds for Medical Sciences (CIFMS) [2021-I2M-1-022], the National Science Foundation of China [81872966], and the National Science &Technology Fundamental Resources Investigation Program of China [2018FY100705]. The funders were not involved in the study design, data collection, analysis, decision to be published, or manuscript preparation.

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  1. Chang Zhang, Mei Jiang contributed equally to this work.

Authors and Affiliations

  1. Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, 100193, Beijing, China

    Chang Zhang, Mei Jiang, Jingting Liu, Bin Wu & Chang Liu

  2. School of Pharmaceutical Sciences, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China

    Mei Jiang

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  1. Chang Zhang
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Zhang, C., Jiang, M., Liu, J. et al. Genome-wide view and characterization of natural antisense transcripts in Cannabis Sativa L. Plant Mol Biol 114, 47 (2024). https://doi.org/10.1007/s11103-024-01434-z

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